public class ModificationLocalizationParameters extends Object implements Serializable
Constructor and Description |
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ModificationLocalizationParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(ModificationLocalizationParameters otherPtmScoringParameters)
Returns true if the objects have identical settings.
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boolean |
getAlignNonConfidentPTMs()
Indicates whether the non confidently localized PTMs should be aligned on
the confident sites.
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double |
getProbabilisticScoreThreshold()
Returns the probabilistic score threshold.
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ModificationLocalizationScore |
getSelectedProbabilisticScore()
Returns the selected probabilistic score.
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SequenceMatchingParameters |
getSequenceMatchingParameters()
Returns the sequence matching preferences to use when mapping PTMs on
amino acid sequences.
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String |
getShortDescription()
Returns a short description of the parameters.
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boolean |
isProbabilisticScoreCalculation()
Indicates whether a probabilistic PTM score is required.
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boolean |
isProbabilisticScoreNeutralLosses()
Indicates whether the neutral losses shall be taken into account for
spectrum annotation when calculating the probabilistic score.
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void |
setAlignNonConfidentPTMs(boolean alignNonConfidentPTMs)
Sets whether the non confidently localized PTMs should be aligned on the
confident sites.
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void |
setProbabilisticScoreCalculation(boolean probabilisticScoreCalculation)
Sets whether a probabilistic PTM score is required.
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void |
setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)
Sets whether the neutral losses shall be taken into account for spectrum
annotation when calculating the probabilistic score.
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void |
setProbabilisticScoreThreshold(double probabilisticScoreThreshold)
Sets the probabilistic score threshold.
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void |
setSelectedProbabilisticScore(ModificationLocalizationScore selectedProbabilisticScore)
Sets the selected probabilistic score.
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void |
setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
Sets the sequence matching preferences to use when mapping PTMs on amino
acid sequences.
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public ModificationLocalizationParameters()
public boolean isProbabilisticScoreCalculation()
public void setProbabilisticScoreCalculation(boolean probabilisticScoreCalculation)
probabilisticScoreCalculation
- a boolean indicating whether a
probabilistic PTM score is requiredpublic ModificationLocalizationScore getSelectedProbabilisticScore()
public void setSelectedProbabilisticScore(ModificationLocalizationScore selectedProbabilisticScore)
selectedProbabilisticScore
- the selected probabilistic scorepublic double getProbabilisticScoreThreshold()
public void setProbabilisticScoreThreshold(double probabilisticScoreThreshold)
probabilisticScoreThreshold
- the probabilistic score thresholdpublic boolean isProbabilisticScoreNeutralLosses()
public void setProbabilisticScoreNeutralLosses(boolean probabilisticScoreNeutralLosses)
probabilisticScoreNeutralLosses
- indicates whether the neutral
losses shall be taken into account for spectrum annotation when
calculating the probabilistic scorepublic SequenceMatchingParameters getSequenceMatchingParameters()
public void setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
sequenceMatchingParameters
- the sequence matching preferences to
use when mapping PTMs on amino acid sequencespublic boolean getAlignNonConfidentPTMs()
public void setAlignNonConfidentPTMs(boolean alignNonConfidentPTMs)
alignNonConfidentPTMs
- a boolean indicating whether the non
confidently localized PTMs should be aligned on the confident sitespublic String getShortDescription()
public boolean equals(ModificationLocalizationParameters otherPtmScoringParameters)
otherPtmScoringParameters
- the PTMScoringParameters to compare toCopyright © 2018. All rights reserved.